New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library !
BioRuby project
13 months
306
12
156345
0
8
Parser of scientific names !
Dmitry Mozzherin
8 weeks
24
3
83831
0
6
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
11 months
26
8
60768
0
0
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
3 years
15
12
55209
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
3 months
117
48
51173
0
2
Shintaro Katayama
8 months
1
41268
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
5 weeks
16
1
38124
0
28
Http requests to entrez e-utilities
Jared Ning
2 years
8
1
34837
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
3 years
14
5
32747
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
6 years
17
5
30893
0
0
Maf parser for BioRuby
Clayton Wheeler
5 years
10
36
27825
0
0
Gff3 parser for big data !
Pjotr Prins
5 years
7
2
26307
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
2 years
13
1
25669
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
2 years
3
2
24903
4
7
A biogem to submit jobs on a queue
Francesco Strozzi
4 years
5
...
24624
0
0
Interfaces with biomodel search engine !
Niall Beard
5 years
1
...
24338
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
2 years
13
3
21882
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
5 years
4
2
21286
0
0
Ruby parsering for obo files !
Matt Yoder
6 years
5
...
21198
0
9
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
3 years
10
21
17973
0
0
Data mining algorithms for jRuby
arrigonialberto86
4 years
16
3
17848
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
1 week
11
5
17662
0
8
A fast parser for fastq files
Francesco Strozzi
5 years
10
...
16866
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
4 years
14146
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
21 months
42
9
14124
0
0
Low memory sequence emitters
Pjotr Prins
3 years
11
1
13704
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
5 years
2
1
13301
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
3 years
3
...
13175
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
17 months
12946
0
0
Build genome output files
Michael Barton
4 years
7
...
12795
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
5 years
29
15
12765
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
6 years
1
...
12725
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
6 months
2
...
12383
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
4 years
4
...
12363
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
4 years
11
2
12175
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
6 years
1
...
11650
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
5 years
2
...
11483
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
6 years
4
...
11362
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
4 years
7
1
11115
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
11 months
2
...
10987
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
5 years
3
...
10869
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
5 years
8
2
10780
0
0
Parser to work with file formats used in
Ben J Woodcroft
2 years
...
10481
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
2 years
...
10442
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
17 months
1
...
10333
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
3 years
...
10137
0
1
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
5 years
3
...
9669
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
6 years
4
...
9539
0
0
A general purpose framework for scripted handling of development/stable
mjy
4 years
2
1
9526
0
2
Library for visualizing genomic regions !
Jan Aerts
1.4
9 years
22
1
9514
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
6 years
1
...
8713
0
0
Read and manipulate cd-hit clusters
George Githinji
4 years
8339
0
0
Ruby binding for samtools tabix
throwern
4 years
5
1
8161
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
6 years
4
...
8072
0
0
A plugin that allows you to parse large
robsyme
6 years
1
...
7797
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
2 years
7688
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
4 years
2
...
7595
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
6 years
12
...
7497
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
18 months
1
...
7410
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
6 years
40
5
7061
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
14 months
1
6995
0
0
Next-generation mapping of mutations
Dan MacLean
4 years
2
...
6927
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
5 years
13
19
6860
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
4 years
6794
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
5 years
1
1
6752
0
0
Publish scientific results to the semantic web !
Will Strinz
3 years
4
16
6727
0
0
Ruby binding to the ucsc kent utilities
throwern
5 years
2
...
6676
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
7 weeks
16
4
6658
0
53
This biogem is built around krona, a flashy
Ben J. Woodcroft
22 months
1
...
6542
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
9 weeks
...
6416
0
7
Bioinformatics triple-store support
Pjotr Prins
5 years
4
1
6242
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
5 years
2
1
6225
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
6 years
1
...
6044
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
4 months
1
5897
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
4 years
5894
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
4 years
...
5800
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
3 years
1
...
5645
0
0
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
13 months
1
...
5571
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
6 years
1
...
5382
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
5 years
1
...
5202
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
5 years
2
...
5186
0
0
A protparam compatible utility for BioRuby
hryk
4 years
2
1
5186
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
5 years
1
...
4766
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
4 years
2
...
4619
0
0
Biostars data-mining and statistical analysis
Joachim Baran
3 years
4288
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
2 years
2
1
4072
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
8 years
5
...
4038
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
5 months
5
2
3988
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
2 years
2
1
3859
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
22 months
3
...
3825
0
0
Gggenome Ruby client
Mitsuteru Nakao
4 years
1
...
3682
0
0
Ruby ensembl rest api
Alberto Donizetti
4 years
2
...
3635
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
3 years
6
...
3528
0
0
Generalized linear models for statsample
Ankur Goel
4 years
3495
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
8 years
90
1
3351
0
0
Interface for express beta diversity
Ben J. Woodcroft
3 years
...
3301
0
0
Bio-repeatmasker
Andrei Rozanski
3 years
...
3222
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
6 years
4
...
3202
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
6 years
3
...
3184
0
0
Helper methods for reading .delta files
robsyme
2 years
...
3168
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
6 years
1
3129
0
0
A parser for cigar format alignments
Ben J Woodcroft
3 years
4
...
3095
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
9 months
3
...
3071
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
7 years
1
...
3060
0
0
Web server for bio-samtools
homonecloco
3 years
...
3001
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
6 years
1
...
2955
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
6 years
1
...
2901
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
6 years
2
...
2894
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
5 years
4
...
2866
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
6 years
...
2852
0
0
One-line summary of your gem
Toshiaki Katayama
5 years
1
...
2852
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
5 years
4
...
2817
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
5 years
1
...
2799
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
6 years
1
...
2798
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
5 years
1
...
2788
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
5 years
3
1
2786
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
5 years
1
...
2764
0
0
Build graph with jRuby
Matteo Picciolini
5 years
2642
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
16 months
...
2449
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
4 years
...
2344
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
4 years
2
...
2165
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
2 years
...
2151
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
2 years
2093
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
4 years
...
2077
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
3 years
1
...
1871
0
0
Mine publications for gene names
Pjotr Prins
3 years
1
...
1700
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
3 years
1
...
1605
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
3 years
1568
0
0
Tools to work with fasta files, indexed with
homonecloco
3 years
...
1531
0
0
Tools to manipulate blat files from the command
homonecloco
3 years
...
1505
0
5
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
2 years
...
1469
0
0
Api of picard tool
Natapol Pornputtapong
2 years
1379
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
2 years
1322
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
8 years
1317
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
2 years
1099
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
2 years
...
1099
0
0
Basic wrapper for the kallistio mapper
homonecloco
2 years
1
...
1072
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
20 months
...
913
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
20 months
...
857
0
0
Biosql plugin for BioRuby
BioRuby project
16 months
...
620
0
0
Cache gemma with loco
Pjotr Prins
6 weeks
...
401
0
24
BioRuby shell: interactive analysis environment for BioRuby
BioRuby project
4 weeks
...
189
0
6
BioRuby executables: utilities bundled with BioRuby
BioRuby project
4 weeks
...
188
0
2
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2017-10-18
**) number of commits on GitHub (last 7 days & last 90 days)